Abstract: 【Objective】This study aimed to investigate endophytic bacteria from Cistanche deserticola and construct synthetic microbial communities， providing a reference for identifying functional microbial communities that promoted seed germination and improved artificial cultivation efficiency of Cistanche deserticola.【Method】High-throughput isolation and cultivation techniques were employed to isolate， cultivate， and purify bacterial strains from Cistanche deserticola stems. A phylogenetic tree of the bacterial species was constructed using the maximum likelihood method， while the growth-promoting functions of the strains—nitrogen fixation， phosphorus solubilization， siderophore production， and indole acetic acid （IAA） production—were assessed. Based on genome-scale metabolic models， competitive and complementary indexes， as well as metabolite transfer potential between strains were calculated to identify and construct synthetic microbial communities. The effectiveness of synthetic communities was validated through pairwise bacterial plate confrontation assays.【Result】High-throughput sequencing yielded 280 bacterial amplicon sequence variants （ASV）， belonging to 4 phyla， 7 classes， 13 orders， 20 families， and 31 genera. The dominant phylum was Proteobacteria （75.7%）， the dominant class was Gammaproteobacteria （69.4%）， the dominant order was Pseudomonadales （32.1%）， and the dominant family was Pseudomonadaceae （31.0%）. Excluding unclassified genera， the dominant genus was Pseudomonas （31.0%）. Further isolation and cultivation from the bacterial ASV yielded 122 endophytic bacterial strains， belonging to 4 phyla， 4 classes， 8 orders， 10 families， 13 genera， and 24 species. The dominant phylum was Proteobacteria （60.6%）， the dominant genus was Pseudomonas （33.6%）， and the dominant species was Bacillus tequilensis （22.9%）. A total of 23 species （89 strains） and 6 species （33 strains） of endophytic bacteria were isolated from 10% TSB media and R2A media， respectively. Five species—Pseudomonas lactis， Serratia proteamaculans， Pseudomonas rhizophila， Paenarthrobacter aurescens， and Pseudomonas pergaminensis—were isolated on both media. All 24 isolated bacterial species exhibited varying IAA production capabilities， while 70.8%， 58.3%， and 62.5% of the species demonstrated nitrogen fixation， phosphorus solubilization， and siderophore production capabilities， respectively. Analysis of the competitive and complementary indexes among the 24 species revealed that Brevundimonas vesicularis exhibited the weakest competitive interactions with other species， while Serratia proteamaculans showed the strongest competitive interactions. By combining four strains into one group， a total of 10626 synthetic community combinations were constructed from the 24 strains. Ten optimal combinations were identified， with Brevundimonas vesicularis and Acinetobacter halotolerans appearing in two combinations， showing low competition and high complementarity， characterized by metabolites secreted by one strain being utilized by another. In plate confrontation assays， the distance between most colonies uniformly decreased over time without the formation of inhibition zones， indicating no antagonistic interactions among the strains.【Conclusion】Based on high-throughput isolation and cultivation techniques， 122 strains representing 24 species of endophytic bacteria with IAA-producing capabilities are isolated， purified， and cultivated. Ultimately， ten synthetic microbial communities with significant metabolic complementarity are identified and thus recommended for further field validation.